By Josh Gordon and State Political Editor

Tony Abbott's decision to hand over $3 billion of public money for the East West Link without a rigorous benefit-cost analysis will be formally investigated by the national audit office.

Auditor-General Ian McPhee is apparently so keen to pursue the issue after making preliminary inquiries with Infrastructure Australia and the Department of Infrastructure that he adjusted the audit work program to accelerate his investigation.

In a letter to opposition infrastructure spokesman Anthony Albanese, Mr McPhee says the audit will examine whether the commitment of the public money for both sections of the controversial road link had been informed by "appropriate advice" and "sound governance arrangements".

"Scheduling this audit has necessarily required some adjustment in our audit work program, but I have done this in view of the considerable commitment of Commonwealth Government funding made towards the project and the importance of the processes established at Commonwealth level to assess the merits of national significant infrastructure investments," Mr McPhee writes.

Mr Abbott committed $3 billion for both sections of the toll road in last year's federal budget, including two cheques worth $1.5 billion handed to the former Napthine government as advance payments in June 2014.

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To offset the cost, the government dumped funding set aside for several other Victorian infrastructure projects, including an upgrade to the M80, the Melbourne metro rail project and funding for a Managed Motorways Project using smart signalling technology to better manage roads.

The promise of $3 billion appeared to breach a Federal Coalition promise made before the 2013 election that there would be no Commonwealth infrastructure projects of more than $100 million without a rigorous benefit-cost analysis.

Mr Albanese said taxpayers deserved to know what due diligence process Mr Abbott undertook before deciding to fund the project.

"Based on documents released by the Andrews government, the Napthine government sought to conceal its business case from the Commonwealth and then attempted to cook the books to make the East West project look worthwhile," Mr Albanese said.

"It also appears Mr Abbott did nothing to satisfy himself that the project represented value for public money."

The looming audit follows a decision by the Andrews government to release the previously secret business case for the project. It revealed that an initial assessment by the former Napthine government found the project would generate a loss-making return of just 45¢ for every $1 invested.

The figure was later boosted to a still-weak return of $1.40 after a range of other projects and claimed benefits were included in the analysis. In contrast, the Managed Motorways Project, which was dumped to pay for Mr Abbott's East-West promise, was assessed by Infrastructure Australia as likely to return $5 for every $1 invested.

Napthine government cabinet documents revealed the former government decided not to release the full business case to Infrastructure Australia – which independently assesses projects – because it was concerned the low benefit-cost ratio "may be used as a justification for not supporting the project".

Former treasurer Michael O'Brien said the Victorian Coalition had welcomed the Abbott government's support for both sections of the project. "The timing of the provision of the funding was a matter for the Commonwealth," Mr O'Brien said.